Archetype packages are sets of class abilities characters may select in place of some of the normal abilities gained from a class. The concept was first introduced in the Genius Guide to Archer Archetypes, and the archetypes presented in this product are fully compatible with Archer Archetypes (though you certainly don't need that book to use the new material in this product). While we went into a fair amount of detail on how and why we developed archetype packages in Archer Archetypes and don't want to repeat ourselves too much, it's important we cover the basics for people who are first encountering the concept here.
This book was written with the assumption that every class has at least one archetype package built into it which represents a standard set of powers that all members of the class receive (see below for details). It is designed with the premise that one can remove some of the standard abilities of a class and replace them with new options that, while different from what the core rulebook says, have no detrimental effect on the class's mechanical balance or ability to fill it's traditional role in an adventuring team.
An obvious example of an existing archetype package can be seen in the cleric, who gets to pick two domains. These are in addition to the cleric's core abilities (and clerics have a broad range of options even without domains). Even if a player neglected to ever select those domains, the character would be able to perform the cleric's core function and maintain the same role in a well-built team. However, over 20 levels these domains give the cleric access to nine spell slots, eighteen spells known, four special abilities, and in some cases up to two additional class skills or bonus feats.
In the context of this product, the cleric's two domains represent a single archetype package—the Domain Servant. That package becomes just one option a cleric can take, with the new archetypes in this volume representing some alternative options. A player who wants to play a cleric that also has a smattering of arcane spells available to her (perhaps as a priest serving a deity of spells and magic) gives up the Domain Servant archetype package and gains one of the new arcane archetypes described in the following pages instead.
Using Arcane Archetypes
The most basic way to use archetype packages is to allow a character, when taking his first level of a new class, to simply swap the archetype package that is normally part of that class our in favor of one of the new packages from this volume. In other words, characters gain these new abilities by foregoing access to some of their class's traditional abilities. This is limiting, but no more so than most of the other decisions one makes when creating a character. (A cleric, after all, cannot change domains after they've been selected, so why would one be allowed to pick a new archetype package a few levels later?)
Whenever new options are added to a campaign, though, it's a good idea to consider ways to allow existing characters to gain access to them. In this case, that would mean finding a way to let characters swap out some of their long-time abilities in favor of a new archetype package. In our cleric example, a character who had already chosen two domains and used their abilities would give up those powers in favor of those from the new archetype.
This exchange is not entirely beyond logical explanation. If you consider archetypes as being similar to modern day occupations, it's easy to justify a character learning new ones occasionally. As an optional rule, you may allow characters to change one archetype package whenever they gain an even-numbered class level. The GM may require a character to have a source of guidance in order to do this—a character with the desired archetype to act as teacher, a manual of instruction, or even divine inspiration. Upon taking a new archetype package, all abilities, feats, and skill ranks associated with the old archetype package are lost. (The skill ranks can be taken from whatever skills the player prefers when an old archetype is abandoned, and may add them in any configuration that falls within the standard rules for skill ranks when they are gained from a new package.)
While a character losing abilities and skills he once possessed may seem unrealistic, there's no other mechanically balanced option to allow existing characters to gain archetypes. In the case of magic powers, it's no great stretch to say that whatever energy once fueled them is now instead channeled into the new abilities. As for feats and skills, they can be explained as activities that require constant practice. They are not technically "lost" or "forgotten" when the character begins studying new areas of expertise, but the character falls out of practice and becomes unable to perform them sufficiently well, thus he may no longer use them in the game.
These answers may not cover every situation, but for most campaigns they should suffice to explain why a character's abilities suddenly change. (If the campaign, GM, or players do not find these answers satisfactory, they should not use this optional rule. This will result in returning archetype packages to being options that may only be taken when a character first takes a level of a base class, which remains a balanced and viable way to handle these new alternative powers.)